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- PDB-7b6u: Sheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pent... -

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Basic information

Entry
Database: PDB / ID: 7b6u
TitleSheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pentaose and 20 mM 6'-sialyllactosamine
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / polyomavirus / capsid protein / VP1 / glycan complex
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
6'-sialyl-N-acetyllactosamine / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / N-acetyl-alpha-neuraminic acid / Capsid protein VP1
Similarity search - Component
Biological speciesSheep polyomavirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsRustmeier, N.H. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: Biorxiv / Year: 2023
Title: A novel and highly specific Forssman antigen-binding protein from sheep polyomavirus
Authors: Rustmeier, N.H. / Silva, L.M. / Di Maio, A. / Mueller, J.C. / Herrmann, A. / Feizi, T. / Liu, Y. / Stehle, T.
History
DepositionDec 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Capsid protein VP1
BBB: Capsid protein VP1
CCC: Capsid protein VP1
DDD: Capsid protein VP1
EEE: Capsid protein VP1
FFF: Capsid protein VP1
GGG: Capsid protein VP1
HHH: Capsid protein VP1
III: Capsid protein VP1
JJJ: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,95247
Polymers305,77410
Non-polymers13,17737
Water36,4442023
1
AAA: Capsid protein VP1
BBB: Capsid protein VP1
CCC: Capsid protein VP1
DDD: Capsid protein VP1
EEE: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,11222
Polymers152,8875
Non-polymers6,22517
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
FFF: Capsid protein VP1
GGG: Capsid protein VP1
HHH: Capsid protein VP1
III: Capsid protein VP1
JJJ: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,84025
Polymers152,8875
Non-polymers6,95320
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.645, 129.645, 220.431
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 10 molecules AAABBBCCCDDDEEEFFFGGGHHHIIIJJJ

#1: Protein
Capsid protein VP1


Mass: 30577.434 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sheep polyomavirus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3ZCF3

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Sugars , 3 types, 16 molecules

#2: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 674.604 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)- ...2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAca1-3DGalpNAcb1-3DGalpa1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2112h-1b_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O][a2112h-1a_1-5_2*NCC/3=O]/1-2-3-4/a4-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][a-D-Galp]{[(3+1)][b-D-GalpNAc]{[(3+1)][a-D-GalpNAc]{}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 2044 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2023 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: KSCN, PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.7263
pseudo-merohedral22K, H, -L20.2737
ReflectionResolution: 1.9→49.48 Å / Num. obs: 325151 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 31.3 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.1461 / Net I/σ(I): 9.46
Reflection shellResolution: 1.9→2.02 Å / Mean I/σ(I) obs: 1.33 / Num. unique obs: 51994 / CC1/2: 0.441 / Rrim(I) all: 1.223

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y61

6y61


Resolution: 1.901→49.47 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: FREE R-VALUE / ESU R: 0.019 / ESU R Free: 0.019
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1726 3164 1 %
Rwork0.1461 321986 -
all0.1461 --
obs-321986 99.764 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.683 Å2
Baniso -1Baniso -2Baniso -3
1--5.055 Å2-0 Å2-0 Å2
2---5.055 Å2-0 Å2
3---10.111 Å2
Refinement stepCycle: LAST / Resolution: 1.901→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20381 0 893 2023 23297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01321825
X-RAY DIFFRACTIONr_bond_other_d0.0350.01719328
X-RAY DIFFRACTIONr_angle_refined_deg1.651.70729688
X-RAY DIFFRACTIONr_angle_other_deg2.7441.61244990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9452641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10422.3531054
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.507153167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.31915119
X-RAY DIFFRACTIONr_chiral_restr0.0790.23010
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0223985
X-RAY DIFFRACTIONr_gen_planes_other0.0140.024587
X-RAY DIFFRACTIONr_nbd_refined0.1780.23716
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.219164
X-RAY DIFFRACTIONr_nbtor_refined0.1660.210481
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.29294
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.21665
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1340.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.214
X-RAY DIFFRACTIONr_nbd_other0.2710.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.241
X-RAY DIFFRACTIONr_mcbond_it2.1242.75810603
X-RAY DIFFRACTIONr_mcbond_other2.1232.75810602
X-RAY DIFFRACTIONr_mcangle_it2.8914.12813225
X-RAY DIFFRACTIONr_mcangle_other2.8924.12813226
X-RAY DIFFRACTIONr_scbond_it2.422.92711222
X-RAY DIFFRACTIONr_scbond_other2.422.92711223
X-RAY DIFFRACTIONr_scangle_it3.3384.32516461
X-RAY DIFFRACTIONr_scangle_other3.3384.32516462
X-RAY DIFFRACTIONr_lrange_it4.79632.90423512
X-RAY DIFFRACTIONr_lrange_other4.68732.61823158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-1.9510.2992280.24823222X-RAY DIFFRACTION97.2142
1.951-2.0040.2612480.21323136X-RAY DIFFRACTION99.7824
2.004-2.0620.2362120.19222697X-RAY DIFFRACTION99.9607
2.062-2.1250.1992150.16821944X-RAY DIFFRACTION99.9684
2.125-2.1950.232090.17321226X-RAY DIFFRACTION99.9907
2.195-2.2720.1711980.15320631X-RAY DIFFRACTION99.9856
2.272-2.3570.1881750.16419870X-RAY DIFFRACTION99.995
2.357-2.4530.1881870.15519046X-RAY DIFFRACTION100
2.453-2.5620.1982130.14718338X-RAY DIFFRACTION99.9838
2.562-2.6870.1851580.1417529X-RAY DIFFRACTION99.9943
2.687-2.8320.1811660.13616694X-RAY DIFFRACTION100
2.832-3.0030.1791580.14315794X-RAY DIFFRACTION100
3.003-3.2090.1361570.13314813X-RAY DIFFRACTION100
3.209-3.4650.1461190.13413780X-RAY DIFFRACTION100
3.465-3.7940.1541160.1312717X-RAY DIFFRACTION99.9922
3.794-4.2390.126980.11511487X-RAY DIFFRACTION99.9482
4.239-4.8890.12900.10910112X-RAY DIFFRACTION100
4.889-5.9730.154920.1378574X-RAY DIFFRACTION99.9539
5.973-8.3860.134730.1526643X-RAY DIFFRACTION100
8.386-49.470.208520.183733X-RAY DIFFRACTION99.7628

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